SummaryJuvenile myelomonocytic leukaemia (JMML) is a rare myeloproliferative neoplasm requiring haematopoietic stem cell transplantation (HSCT) for potential cure. Relapse poses a significant obstacle to JMML HSCT treatment, as the lack of effective minimal residual disease (MRD)‐monitoring methods leads to delayed interventions. This retrospective study utilized the droplet digital PCR (ddPCR) technique, a highly sensitive nucleic acid detection and quantification technique, to monitor MRD in 32 JMML patients. The results demonstrated that ddPCR detected relapse manifestations earlier than traditional methods and uncovered molecular insights into JMML MRD dynamics. The findings emphasized a critical 1‐ to 3‐month window post‐HSCT for detecting molecular relapse, with 66.7% (8/12) of relapses occurring within this period. Slow MRD clearance post‐HSCT was observed, as 65% (13/20) of non‐relapse patients took over 6 months to achieve ddPCR‐MRD negativity. Furthermore, bone marrow ddPCR‐MRD levels at 1‐month post‐HSCT proved to be prognostically significant. Relapsed patients exhibited significantly elevated ddPCR‐MRD levels at this time point (p = 0.026), with a cut‐off of 0.465% effectively stratifying overall survival (p = 0.007), event‐free survival (p = 0.035) and cumulative incidence of relapse (p = 0.035). In conclusion, this study underscored ddPCR's superiority in JMML MRD monitoring post‐HSCT. It provided valuable insights into JMML MRD dynamics, offering guidance for the effective management of JMML.